Refget: standardized access to reference sequences

Abstract

Abstract Motivation Reference sequences are essential in creating a baseline of knowledge for many common bioinformatics methods, especially those using genomic sequencing. Results We have created refget, a Global Alliance for Genomics and Health API specification to access reference sequences and sub-sequences using an identifier derived from the sequence itself. We present four reference implementations across in-house and cloud infrastructure, a compliance suite and a web report used to ensure specification conformity across implementations. Availability and implementation The refget specification can be found at: https://w3id.org/ga4gh/refget. Supplementary information Supplementary data are available at Bioinformatics online.